diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.cpp b/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.cpp index b7dda3ce9d..c1e2aa0412 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.cpp +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.cpp @@ -1,148 +1,158 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkBooleanOperationsWidget.h" #include +#include #include #include #include #include static const char* const HelpText = "Select two different segmentations above"; namespace { static std::string GetPrefix(mitk::BooleanOperation::Type type) { switch (type) { case mitk::BooleanOperation::Difference: return "DifferenceFrom_"; case mitk::BooleanOperation::Intersection: return "IntersectionWith_"; case mitk::BooleanOperation::Union: return "UnionWith_"; default: assert(false && "Unknown boolean operation type"); return "UNKNOWN_BOOLEAN_OPERATION_WITH_"; } } static void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr) { - auto dataNode = mitk::DataNode::New(); + if (dataStorage.IsNull()) + { + std::string exception = "Cannot add result to the data storage. Data storage invalid."; + MITK_ERROR << "Boolean operation failed: " << exception; + QMessageBox::information(nullptr, "Boolean operation failed", QString::fromStdString(exception)); + } + auto dataNode = mitk::DataNode::New(); dataNode->SetName(name); dataNode->SetData(segmentation); dataStorage->Add(dataNode, parent); } } -QmitkBooleanOperationsWidget::QmitkBooleanOperationsWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) +QmitkBooleanOperationsWidget::QmitkBooleanOperationsWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls = new Ui::QmitkBooleanOperationsWidgetControls; m_Controls->setupUi(this); + m_Controls->dataSelectionWidget->SetDataStorage(dataStorage); m_Controls->dataSelectionWidget->AddDataSelection("", "Select 1st segmentation", "Select 1st segmentation", "", QmitkDataSelectionWidget::SegmentationPredicate); m_Controls->dataSelectionWidget->AddDataSelection("", "Select 2nd segmentation", "Select 2nd segmentation", "", QmitkDataSelectionWidget::SegmentationPredicate); m_Controls->dataSelectionWidget->SetHelpText(HelpText); connect(m_Controls->dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); connect(m_Controls->differenceButton, SIGNAL(clicked()), this, SLOT(OnDifferenceButtonClicked())); connect(m_Controls->intersectionButton, SIGNAL(clicked()), this, SLOT(OnIntersectionButtonClicked())); connect(m_Controls->unionButton, SIGNAL(clicked()), this, SLOT(OnUnionButtonClicked())); } QmitkBooleanOperationsWidget::~QmitkBooleanOperationsWidget() { } void QmitkBooleanOperationsWidget::OnSelectionChanged(unsigned int, const mitk::DataNode*) { auto dataSelectionWidget = m_Controls->dataSelectionWidget; auto nodeA = dataSelectionWidget->GetSelection(0); auto nodeB = dataSelectionWidget->GetSelection(1); if (nodeA.IsNotNull() && nodeB.IsNotNull() && nodeA != nodeB) { dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } else { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } } void QmitkBooleanOperationsWidget::EnableButtons(bool enable) { m_Controls->differenceButton->setEnabled(enable); m_Controls->intersectionButton->setEnabled(enable); m_Controls->unionButton->setEnabled(enable); } void QmitkBooleanOperationsWidget::OnDifferenceButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Difference); } void QmitkBooleanOperationsWidget::OnIntersectionButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Intersection); } void QmitkBooleanOperationsWidget::OnUnionButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Union); } void QmitkBooleanOperationsWidget::DoBooleanOperation(mitk::BooleanOperation::Type type) { auto timeNavigationController = this->GetTimeNavigationController(); assert(timeNavigationController != nullptr); mitk::Image::Pointer segmentationA = dynamic_cast(m_Controls->dataSelectionWidget->GetSelection(0)->GetData()); mitk::Image::Pointer segmentationB = dynamic_cast(m_Controls->dataSelectionWidget->GetSelection(1)->GetData()); mitk::Image::Pointer result; try { mitk::BooleanOperation booleanOperation(type, segmentationA, segmentationB, timeNavigationController->GetSelectedTimePoint()); result = booleanOperation.GetResult(); assert(result.IsNotNull()); auto dataSelectionWidget = m_Controls->dataSelectionWidget; AddToDataStorage( dataSelectionWidget->GetDataStorage(), result, GetPrefix(type) + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); } catch (const mitk::Exception& exception) { MITK_ERROR << "Boolean operation failed: " << exception.GetDescription(); QMessageBox::information(nullptr, "Boolean operation failed", exception.GetDescription()); } } diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.h b/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.h index 7a9fc0cde4..29b0e89e87 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.h +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkBooleanOperationsWidget.h @@ -1,52 +1,55 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkBooleanOperationsWidget_h #define QmitkBooleanOperationsWidget_h #include #include #include namespace Ui { class QmitkBooleanOperationsWidgetControls; } namespace mitk { class DataNode; + class DataStorage; } class MITKSEGMENTATIONUI_EXPORT QmitkBooleanOperationsWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: - explicit QmitkBooleanOperationsWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); + explicit QmitkBooleanOperationsWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent = nullptr); ~QmitkBooleanOperationsWidget() override; private slots: void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); void OnDifferenceButtonClicked(); void OnIntersectionButtonClicked(); void OnUnionButtonClicked(); private: void EnableButtons(bool enable = true); void DoBooleanOperation(mitk::BooleanOperation::Type type); Ui::QmitkBooleanOperationsWidgetControls* m_Controls; }; #endif diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.cpp b/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.cpp index d0c65a7548..883633b384 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.cpp +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.cpp @@ -1,247 +1,259 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkContourModelToImageWidget.h" #include +#include #include #include #include #include #include #include #include #include #include static const char* const HelpText = "Select a image and a contour(set)"; class QmitkContourModelToImageWidgetPrivate { public: QmitkContourModelToImageWidgetPrivate(); ~QmitkContourModelToImageWidgetPrivate(); /** @brief Check if selections is valid. */ void SelectionControl( unsigned int index, const mitk::DataNode* selection); /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Does the actual contour filling */ mitk::LabelSetImage::Pointer FillContourModelSetIntoImage(mitk::Image *image, mitk::ContourModelSet *contourSet, mitk::TimePointType timePoint); Ui::QmitkContourModelToImageWidgetControls m_Controls; QFutureWatcher m_Watcher; }; QmitkContourModelToImageWidgetPrivate::QmitkContourModelToImageWidgetPrivate() { } QmitkContourModelToImageWidgetPrivate::~QmitkContourModelToImageWidgetPrivate() { } void QmitkContourModelToImageWidgetPrivate::EnableButtons(bool enable) { m_Controls.btnProcess->setEnabled(enable); } void QmitkContourModelToImageWidgetPrivate::SelectionControl(unsigned int index, const mitk::DataNode* /*selection*/) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } mitk::LabelSetImage::Pointer QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage(mitk::Image* image, mitk::ContourModelSet* contourSet, mitk::TimePointType timePoint) { // Use mitk::ContourModelSetToImageFilter to fill the ContourModelSet into the image mitk::ContourModelSetToImageFilter::Pointer contourFiller = mitk::ContourModelSetToImageFilter::New(); auto timeStep = image->GetTimeGeometry()->TimePointToTimeStep(timePoint); contourFiller->SetTimeStep(timeStep); contourFiller->SetImage(image); contourFiller->SetInput(contourSet); contourFiller->MakeOutputBinaryOn(); try { contourFiller->Update(); } catch (const std::exception & e) { MITK_ERROR << "Error while converting contour model. "<< e.what(); } catch (...) { MITK_ERROR << "Unknown error while converting contour model."; } if (nullptr == contourFiller->GetOutput()) { MITK_ERROR<<"Could not write the selected contours into the image!"; } auto result = mitk::LabelSetImage::New(); result->InitializeByLabeledImage(contourFiller->GetOutput()); return result; } void QmitkContourModelToImageWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) { Q_D(QmitkContourModelToImageWidget); QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNull() || node1.IsNull() ) { d->EnableButtons(false); dataSelectionWidget->SetHelpText(HelpText); } else { d->SelectionControl(index, selection); } } void QmitkContourModelToImageWidget::OnProcessingFinished() { // Called when processing finished // Adding the result to the data storage Q_D(QmitkContourModelToImageWidget); // Adding the result to the data storage auto result = d->m_Watcher.result(); if (result.IsNotNull()) { QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer contourNode = dataSelectionWidget->GetSelection(1); mitk::DataNode::Pointer filled = mitk::DataNode::New(); std::stringstream stream; stream << imageNode->GetName(); stream << "_"; stream << contourNode->GetName(); filled->SetName(stream.str()); filled->SetData(result); - dataSelectionWidget->GetDataStorage()->Add(filled, imageNode); + auto dataStorage = dataSelectionWidget->GetDataStorage(); + if (dataStorage.IsNull()) + { + std::string exception = "Cannot add result to the data storage. Data storage invalid."; + MITK_ERROR << "Error filling contours into an image: " << exception; + QMessageBox::information(nullptr, "Error filling contours into an image", QString::fromStdString(exception)); + } + + dataStorage->Add(filled, imageNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else { MITK_ERROR<<"Error filling contours into an image!"; } d->EnableButtons(); } void QmitkContourModelToImageWidget::OnProcessPressed() { Q_D(QmitkContourModelToImageWidget); QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer contourNode = dataSelectionWidget->GetSelection(1); // Check if data nodes are valid if(imageNode.IsNull() || contourNode.IsNull() ) { MITK_ERROR << "Selection does not contain valid data"; QMessageBox::information( this, "Contour To Image", "Selection does not contain valid data, please select a binary image and a contour(set)", QMessageBox::Ok ); d->m_Controls.btnProcess->setEnabled(false); return; } mitk::Image::Pointer image = static_cast(imageNode->GetData()); // Check if the image is valid if (image.IsNull()) { MITK_ERROR<<"Error writing contours into image! Invalid image data selected!"; return; } const auto timePoint = this->GetTimeNavigationController()->GetSelectedTimePoint(); if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_ERROR << "Error writing contours into image! Currently selected time point is not supported by selected image data."; return; } // Check if the selected contours are valid mitk::ContourModelSet::Pointer contourSet; mitk::ContourModel::Pointer contour = dynamic_cast(contourNode->GetData()); if (contour.IsNotNull()) { contourSet = mitk::ContourModelSet::New(); contourSet->AddContourModel(contour); } else { contourSet = static_cast(contourNode->GetData()); if (contourSet.IsNull()) { MITK_ERROR<<"Error writing contours into binary image! Invalid contour data selected!"; return; } } //Disable Buttons during calculation and initialize Progressbar d->EnableButtons(false); // Start the computation in a background thread QFuture< mitk::LabelSetImage::Pointer > future = QtConcurrent::run(d, &QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage, image, contourSet, timePoint); d->m_Watcher.setFuture(future); } -QmitkContourModelToImageWidget::QmitkContourModelToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) +QmitkContourModelToImageWidget::QmitkContourModelToImageWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent), d_ptr(new QmitkContourModelToImageWidgetPrivate()) { Q_D(QmitkContourModelToImageWidget); // Set up UI d->m_Controls.setupUi(this); + d->m_Controls.dataSelectionWidget->SetDataStorage(dataStorage); d->m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImageAndSegmentationPredicate); d->m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ContourModelPredicate); d->m_Controls.dataSelectionWidget->SetHelpText(HelpText); d->EnableButtons(false); // Create connections connect (d->m_Controls.btnProcess, SIGNAL(pressed()), this, SLOT(OnProcessPressed())); connect(d->m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); connect(&d->m_Watcher, SIGNAL(finished()), this, SLOT(OnProcessingFinished())); if( d->m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && d->m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { OnSelectionChanged(0, d->m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkContourModelToImageWidget::~QmitkContourModelToImageWidget() { } diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.h b/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.h index f71d2635a9..562d254434 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.h +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkContourModelToImageWidget.h @@ -1,73 +1,76 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkContourModelToImageWidget_h #define QmitkContourModelToImageWidget_h #include #include #include class QmitkContourModelToImageWidgetPrivate; namespace mitk { class DataNode; + class DataStorage; class Image; class ContourModelSet; class ContourModel; class Geometry3D; class PlaneGeometry; } /*! \brief QmitkContourModelToImageWidget Tool masks an image with a binary image or a surface. The Method requires an image and a binary image mask or a surface. The input image and the binary image mask must be of the same size. Masking with a surface creates first a binary image of the surface and then use this for the masking of the input image. */ class MITKSEGMENTATIONUI_EXPORT QmitkContourModelToImageWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ - explicit QmitkContourModelToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); + explicit QmitkContourModelToImageWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent = nullptr); /** @brief Defaul destructor. */ ~QmitkContourModelToImageWidget() override; private slots: /** @brief This slot is called if the selection in the workbench is changed. */ void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); /** @brief This slot is called if user activates the button to mask an image. */ void OnProcessPressed(); /** @brief This slot is called after processing is finished */ void OnProcessingFinished(); private: QScopedPointer d_ptr; Q_DECLARE_PRIVATE(QmitkContourModelToImageWidget) Q_DISABLE_COPY(QmitkContourModelToImageWidget) }; #endif diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.cpp b/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.cpp index e9e2d4e162..2b0aaaafc8 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.cpp +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.cpp @@ -1,240 +1,242 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkDataSelectionWidget.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include static mitk::NodePredicateBase::Pointer CreatePredicate(QmitkDataSelectionWidget::Predicate predicate) { auto imageType = mitk::TNodePredicateDataType::New(); auto labelSetImageType = mitk::TNodePredicateDataType::New(); auto surfaceType = mitk::TNodePredicateDataType::New(); auto contourModelType = mitk::TNodePredicateDataType::New(); auto contourModelSetType = mitk::TNodePredicateDataType::New(); auto nonLabelSetImageType = mitk::NodePredicateAnd::New(imageType, mitk::NodePredicateNot::New(labelSetImageType)); auto nonHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateOr::New( mitk::NodePredicateProperty::New("helper object"), mitk::NodePredicateProperty::New("hidden object"))); auto isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); auto isSegmentation = mitk::NodePredicateProperty::New("segmentation", mitk::BoolProperty::New(true)); auto isBinaryOrSegmentation = mitk::NodePredicateOr::New(isBinary, isSegmentation); mitk::NodePredicateBase::Pointer returnValue; switch(predicate) { case QmitkDataSelectionWidget::ImagePredicate: returnValue = mitk::NodePredicateAnd::New( mitk::NodePredicateNot::New(isBinaryOrSegmentation), nonLabelSetImageType).GetPointer(); break; case QmitkDataSelectionWidget::SegmentationPredicate: returnValue = mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(imageType, isBinaryOrSegmentation), labelSetImageType).GetPointer(); break; case QmitkDataSelectionWidget::SurfacePredicate: returnValue = surfaceType.GetPointer(); break; case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: returnValue = imageType.GetPointer(); break; case QmitkDataSelectionWidget::ContourModelPredicate: returnValue = mitk::NodePredicateOr::New( contourModelSetType, contourModelSetType).GetPointer(); break; case QmitkDataSelectionWidget::SegmentationOrSurfacePredicate: returnValue = mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(imageType, isBinaryOrSegmentation), labelSetImageType).GetPointer(); returnValue = mitk::NodePredicateOr::New(returnValue, surfaceType).GetPointer(); break; default: assert(false && "Unknown predefined predicate!"); return nullptr; } return mitk::NodePredicateAnd::New(returnValue, nonHelperObject).GetPointer(); } QmitkDataSelectionWidget::QmitkDataSelectionWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.helpLabel->hide(); } QmitkDataSelectionWidget::~QmitkDataSelectionWidget() { } unsigned int QmitkDataSelectionWidget::AddDataSelection(QmitkDataSelectionWidget::Predicate predicate) { QString hint = "Select node"; switch (predicate) { case QmitkDataSelectionWidget::ImagePredicate: hint = "Select an image"; break; case QmitkDataSelectionWidget::SegmentationPredicate: hint = "Select a segmentation"; break; case QmitkDataSelectionWidget::SurfacePredicate: hint = "Select a surface"; break; case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: hint = "Select an image or segmentation"; break; case QmitkDataSelectionWidget::ContourModelPredicate: hint = "Select a contour model"; break; case QmitkDataSelectionWidget::SegmentationOrSurfacePredicate: hint = "Select a segmentation or surface"; break; } return this->AddDataSelection("", hint, hint, "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(mitk::NodePredicateBase* predicate) { return this->AddDataSelection("", "Select a node", "Select a node", "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, QmitkDataSelectionWidget::Predicate predicate) { return this->AddDataSelection(labelText, info, popupHint, popupTitel, CreatePredicate(predicate)); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate) { int row = m_Controls.gridLayout->rowCount(); if (!labelText.isEmpty()) { QLabel* label = new QLabel(labelText, m_Controls.dataSelectionWidget); label->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); m_Controls.gridLayout->addWidget(label, row, 0); } QmitkSingleNodeSelectionWidget* nodeSelection = new QmitkSingleNodeSelectionWidget(m_Controls.dataSelectionWidget); nodeSelection->SetSelectionIsOptional(false); nodeSelection->SetInvalidInfo(info); nodeSelection->SetPopUpTitel(popupTitel); nodeSelection->SetPopUpHint(popupHint); nodeSelection->SetDataStorage(this->GetDataStorage()); nodeSelection->SetNodePredicate(predicate); nodeSelection->SetAutoSelectNewNodes(true); nodeSelection->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); nodeSelection->setMinimumSize(0, 40); connect(nodeSelection, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkDataSelectionWidget::OnSelectionChanged); m_Controls.gridLayout->addWidget(nodeSelection, row, 1); m_NodeSelectionWidgets.push_back(nodeSelection); return static_cast(m_NodeSelectionWidgets.size() - 1); return row; } -mitk::DataStorage::Pointer QmitkDataSelectionWidget::GetDataStorage() const +void QmitkDataSelectionWidget::SetDataStorage(mitk::DataStorage* dataStorage) { - //ctkServiceReference ref = mitk::PluginActivator::getContext()->getServiceReference(); - //assert(ref == true); - - //mitk::IDataStorageService* service = mitk::PluginActivator::getContext()->getService(ref); + if (m_DataStorage == dataStorage) + { + return; + } - //assert(service); + m_DataStorage = dataStorage; +} - //return service->GetDefaultDataStorage()->GetDataStorage(); - return nullptr; +mitk::DataStorage::Pointer QmitkDataSelectionWidget::GetDataStorage() const +{ + return m_DataStorage.Lock(); } mitk::DataNode::Pointer QmitkDataSelectionWidget::GetSelection(unsigned int index) { assert(index < m_NodeSelectionWidgets.size()); return m_NodeSelectionWidgets[index]->GetSelectedNode(); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, Predicate predicate) { this->SetPredicate(index, CreatePredicate(predicate)); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, const mitk::NodePredicateBase* predicate) { assert(index < m_NodeSelectionWidgets.size()); m_NodeSelectionWidgets[index]->SetNodePredicate(predicate); } const mitk::NodePredicateBase *QmitkDataSelectionWidget::GetPredicate(unsigned int index) const { assert(index < m_NodeSelectionWidgets.size()); return m_NodeSelectionWidgets[index]->GetNodePredicate(); } void QmitkDataSelectionWidget::SetHelpText(const QString& text) { if (!text.isEmpty()) { m_Controls.helpLabel->setText(text); if (!m_Controls.helpLabel->isVisible()) m_Controls.helpLabel->show(); } else { m_Controls.helpLabel->hide(); } } void QmitkDataSelectionWidget::OnSelectionChanged(QList selection) { std::vector::iterator it = std::find(m_NodeSelectionWidgets.begin(), m_NodeSelectionWidgets.end(), sender()); assert(it != m_NodeSelectionWidgets.end()); const mitk::DataNode* result = nullptr; if (!selection.empty()) { result = selection.front(); } emit SelectionChanged(std::distance(m_NodeSelectionWidgets.begin(), it), result); } diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.h b/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.h index 3d1894172e..4195fd235d 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.h +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkDataSelectionWidget.h @@ -1,71 +1,75 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkDataSelectionWidget_h #define QmitkDataSelectionWidget_h #include #include #include #include +#include + #include namespace mitk { class NodePredicateBase; } class QmitkSingleNodeSelectionWidget; class MITKSEGMENTATIONUI_EXPORT QmitkDataSelectionWidget : public QWidget { Q_OBJECT public: enum Predicate { ImagePredicate, SegmentationPredicate, SurfacePredicate, ImageAndSegmentationPredicate, ContourModelPredicate, SegmentationOrSurfacePredicate }; explicit QmitkDataSelectionWidget(QWidget* parent = nullptr); ~QmitkDataSelectionWidget() override; unsigned int AddDataSelection(Predicate predicate); unsigned int AddDataSelection(mitk::NodePredicateBase* predicate = nullptr); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, Predicate predicate); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate = nullptr); + void SetDataStorage(mitk::DataStorage* dataStorage); mitk::DataStorage::Pointer GetDataStorage() const; mitk::DataNode::Pointer GetSelection(unsigned int index); void SetPredicate(unsigned int index, Predicate predicate); void SetPredicate(unsigned int index, const mitk::NodePredicateBase* predicate); const mitk::NodePredicateBase *GetPredicate(unsigned int index) const; void SetHelpText(const QString& text); signals: void SelectionChanged(unsigned int index, const mitk::DataNode* selection); private slots: void OnSelectionChanged(QList selection); private: Ui::QmitkDataSelectionWidgetControls m_Controls; + mitk::WeakPointer m_DataStorage; std::vector m_NodeSelectionWidgets; }; #endif diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.cpp b/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.cpp index 3bad8132da..0e542d4d04 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.cpp +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.cpp @@ -1,383 +1,393 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkImageMaskingWidget.h" #include +#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace { bool IsSurface(const mitk::DataNode* dataNode) { if (nullptr != dataNode) { if (nullptr != dynamic_cast(dataNode->GetData())) return true; } return false; } } static const char* const HelpText = "Select an image and a segmentation or surface"; -QmitkImageMaskingWidget::QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) +QmitkImageMaskingWidget::QmitkImageMaskingWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls = new Ui::QmitkImageMaskingWidgetControls; m_Controls->setupUi(this); + m_Controls->dataSelectionWidget->SetDataStorage(dataStorage); m_Controls->dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImagePredicate); m_Controls->dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::SegmentationOrSurfacePredicate); m_Controls->dataSelectionWidget->SetHelpText(HelpText); // T28795: Disable 2-d reference images since they do not work yet (segmentations are at least 3-d images with a single slice) m_Controls->dataSelectionWidget->SetPredicate(0, mitk::NodePredicateAnd::New( mitk::NodePredicateNot::New(mitk::NodePredicateDimension::New(2)), m_Controls->dataSelectionWidget->GetPredicate(0))); this->EnableButtons(false); connect(m_Controls->btnMaskImage, SIGNAL(clicked()), this, SLOT(OnMaskImagePressed())); connect(m_Controls->rbnCustom, SIGNAL(toggled(bool)), this, SLOT(OnCustomValueButtonToggled(bool))); connect(m_Controls->dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if( m_Controls->dataSelectionWidget->GetSelection(0).IsNotNull() && m_Controls->dataSelectionWidget->GetSelection(1).IsNotNull() ) { this->OnSelectionChanged(0, m_Controls->dataSelectionWidget->GetSelection(0)); } } QmitkImageMaskingWidget::~QmitkImageMaskingWidget() { } void QmitkImageMaskingWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode *selection) { auto *dataSelectionWidget = m_Controls->dataSelectionWidget; auto node0 = dataSelectionWidget->GetSelection(0); if (index == 0) { dataSelectionWidget->SetPredicate(1, QmitkDataSelectionWidget::SegmentationOrSurfacePredicate); if (node0.IsNotNull()) { dataSelectionWidget->SetPredicate(1, mitk::NodePredicateAnd::New( mitk::NodePredicateGeometry::New(node0->GetData()->GetGeometry()), dataSelectionWidget->GetPredicate(1))); } } auto node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNull() || node1.IsNull()) { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } else { this->SelectionControl(index, selection); } } void QmitkImageMaskingWidget::SelectionControl(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); //if Image-Masking is enabled, check if image-dimension of reference and binary image is identical if( !IsSurface(dataSelectionWidget->GetSelection(1)) ) { if( dataSelectionWidget->GetSelection(0) == dataSelectionWidget->GetSelection(1) ) { dataSelectionWidget->SetHelpText("Select two different images above"); this->EnableButtons(false); return; } else if( node.IsNotNull() && selection ) { mitk::Image::Pointer referenceImage = dynamic_cast ( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Image::Pointer maskImage = dynamic_cast ( dataSelectionWidget->GetSelection(1)->GetData() ); if (maskImage.IsNull()) { dataSelectionWidget->SetHelpText("Different image sizes cannot be masked"); this->EnableButtons(false); return; } } else { dataSelectionWidget->SetHelpText(HelpText); return; } } dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } void QmitkImageMaskingWidget::EnableButtons(bool enable) { m_Controls->grpBackgroundValue->setEnabled(enable); m_Controls->btnMaskImage->setEnabled(enable); } template void GetRange(const itk::Image*, double& bottom, double& top) { bottom = std::numeric_limits::lowest(); top = std::numeric_limits::max(); } void QmitkImageMaskingWidget::OnCustomValueButtonToggled(bool checked) { m_Controls->txtCustom->setEnabled(checked); } void QmitkImageMaskingWidget::OnMaskImagePressed() { //Disable Buttons during calculation and initialize Progressbar this->EnableButtons(false); mitk::ProgressBar::GetInstance()->AddStepsToDo(4); mitk::ProgressBar::GetInstance()->Progress(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; //create result image, get mask node and reference image mitk::Image::Pointer resultImage(nullptr); mitk::DataNode::Pointer maskingNode = dataSelectionWidget->GetSelection(1); mitk::Image::Pointer referenceImage = static_cast(dataSelectionWidget->GetSelection(0)->GetData()); if(referenceImage.IsNull() || maskingNode.IsNull() ) { MITK_ERROR << "Selection does not contain an image"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain an image", QMessageBox::Ok ); m_Controls->btnMaskImage->setEnabled(true); return; } //Do Image-Masking if (!IsSurface(maskingNode)) { mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer maskImage = dynamic_cast ( maskingNode->GetData() ); if(maskImage.IsNull() ) { MITK_ERROR << "Selection does not contain a segmentation"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a segmentation", QMessageBox::Ok ); this->EnableButtons(); return; } resultImage = this->MaskImage(referenceImage, maskImage); } //Do Surface-Masking else { mitk::ProgressBar::GetInstance()->Progress(); //1. convert surface to image mitk::Surface::Pointer surface = dynamic_cast ( maskingNode->GetData() ); //TODO Get 3D Surface of current time step if(surface.IsNull()) { MITK_ERROR << "Selection does not contain a surface"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a surface", QMessageBox::Ok ); this->EnableButtons(); return; } mitk::Image::Pointer maskImage = this->ConvertSurfaceToImage( referenceImage, surface ); //2. mask reference image with mask image if(maskImage.IsNotNull() && referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) { resultImage = this->MaskImage( referenceImage, maskImage ); } } mitk::ProgressBar::GetInstance()->Progress(); if( resultImage.IsNull() ) { MITK_ERROR << "Masking failed"; QMessageBox::information( this, "Image and Surface Masking", "Masking failed. For more information please see logging window.", QMessageBox::Ok ); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(4); return; } //Add result to data storage this->AddToDataStorage( dataSelectionWidget->GetDataStorage(), resultImage, dataSelectionWidget->GetSelection(0)->GetName() + "_" + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(); } mitk::Image::Pointer QmitkImageMaskingWidget::MaskImage(mitk::Image::Pointer referenceImage, mitk::Image::Pointer maskImage ) { mitk::ScalarType backgroundValue = 0.0; if (m_Controls->rbnMinimum->isChecked()) { backgroundValue = referenceImage->GetStatistics()->GetScalarValueMin(); } else if (m_Controls->rbnCustom->isChecked()) { auto warningTitle = QStringLiteral("Invalid custom pixel value"); bool ok = false; auto originalBackgroundValue = m_Controls->txtCustom->text().toDouble(&ok); if (!ok) { // Input is not even a number QMessageBox::warning(nullptr, warningTitle, "Please enter a valid number as custom pixel value."); return nullptr; } else { // Clamp to the numerical limits of the pixel/component type double bottom, top; if (referenceImage->GetDimension() == 4) { AccessFixedDimensionByItk_n(referenceImage, GetRange, 4, (bottom, top)); } else { AccessByItk_n(referenceImage, GetRange, (bottom, top)); } backgroundValue = std::max(bottom, std::min(originalBackgroundValue, top)); // Get rid of decimals for integral numbers auto type = referenceImage->GetPixelType().GetComponentType(); if (type != itk::IOComponentEnum::FLOAT && type != itk::IOComponentEnum::DOUBLE) backgroundValue = std::round(backgroundValue); } // Ask the user for permission before correcting their input if (std::abs(originalBackgroundValue - backgroundValue) > 1e-4) { auto warningText = QString( "

The custom pixel value %1 lies not within the range of valid pixel values for the selected image.

" "

Apply the closest valid pixel value %2 instead?

").arg(originalBackgroundValue).arg(backgroundValue); auto ret = QMessageBox::warning( nullptr, warningTitle, warningText, QMessageBox::StandardButton::Apply | QMessageBox::StandardButton::Cancel, QMessageBox::StandardButton::Apply); if (QMessageBox::StandardButton::Apply != ret) return nullptr; m_Controls->txtCustom->setText(QString("%1").arg(backgroundValue)); } } auto maskFilter = mitk::MaskImageFilter::New(); maskFilter->SetInput(referenceImage); maskFilter->SetMask(maskImage); maskFilter->OverrideOutsideValueOn(); maskFilter->SetOutsideValue(backgroundValue); try { maskFilter->Update(); } catch(const itk::ExceptionObject& e) { MITK_ERROR << e.GetDescription(); return nullptr; } return maskFilter->GetOutput(); } mitk::Image::Pointer QmitkImageMaskingWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ) { mitk::ProgressBar::GetInstance()->AddStepsToDo(2); mitk::ProgressBar::GetInstance()->Progress(); mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->MakeOutputBinaryOn(); surfaceToImageFilter->SetInput(surface); surfaceToImageFilter->SetImage(image); try { surfaceToImageFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return nullptr; } mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer resultImage = mitk::Image::New(); resultImage = surfaceToImageFilter->GetOutput(); return resultImage; } void QmitkImageMaskingWidget::AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent ) { - auto dataNode = mitk::DataNode::New(); + if (dataStorage.IsNull()) + { + std::string exception = "Cannot add result to the data storage. Data storage invalid."; + MITK_ERROR << "Masking failed: " << exception; + QMessageBox::information(nullptr, "Masking failed", QString::fromStdString(exception)); + } + auto dataNode = mitk::DataNode::New(); dataNode->SetName(name); dataNode->SetData(segmentation); if (parent.IsNotNull()) { mitk::LevelWindow levelWindow; parent->GetLevelWindow(levelWindow); dataNode->SetLevelWindow(levelWindow); } dataStorage->Add(dataNode, parent); } diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.h b/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.h index e037f8324b..b8be1847bf 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.h +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkImageMaskingWidget.h @@ -1,84 +1,87 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkImageMaskingWidget_h #define QmitkImageMaskingWidget_h #include #include #include #include namespace Ui { class QmitkImageMaskingWidgetControls; } namespace mitk { + class DataStorage; class Image; } /*! \brief QmitkImageMaskingWidget Tool masks an image with a binary image or a surface. The Method requires an image and a binary image mask or a surface. The input image and the binary image mask must be of the same size. Masking with a surface creates first a binary image of the surface and then use this for the masking of the input image. */ class MITKSEGMENTATIONUI_EXPORT QmitkImageMaskingWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ - explicit QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); + explicit QmitkImageMaskingWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent = nullptr); /** @brief Defaul destructor. */ ~QmitkImageMaskingWidget() override; private slots: /** @brief This slot is called if the selection in the workbench is changed. */ void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); /** @brief This slot is called if user activates the button to mask an image. */ void OnMaskImagePressed(); /** @brief This slot is called if the user toggles the "Custom" radio button. */ void OnCustomValueButtonToggled(bool checked); private: /** @brief Check if selections is valid. */ void SelectionControl( unsigned int index, const mitk::DataNode* selection); /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Mask an image with a given binary mask. Note that the input image and the mask image must be of the same size. */ itk::SmartPointer MaskImage(itk::SmartPointer referenceImage, itk::SmartPointer maskImage ); /** @brief Convert a surface into an binary image. */ itk::SmartPointer ConvertSurfaceToImage( itk::SmartPointer image, mitk::Surface::Pointer surface ); /** @brief Adds a new data object to the DataStorage.*/ void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, itk::SmartPointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr); Ui::QmitkImageMaskingWidgetControls* m_Controls; }; #endif diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp b/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp index 61a3e2a942..b02a5ea938 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp @@ -1,255 +1,258 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkMorphologicalOperationsWidget.h" #include #include #include #include static const char* const HelpText = "Select a segmentation above"; -QmitkMorphologicalOperationsWidget::QmitkMorphologicalOperationsWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) +QmitkMorphologicalOperationsWidget::QmitkMorphologicalOperationsWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls = new Ui::QmitkMorphologicalOperationsWidgetControls; m_Controls->setupUi(this); + m_Controls->dataSelectionWidget->SetDataStorage(dataStorage); m_Controls->dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::SegmentationPredicate); m_Controls->dataSelectionWidget->SetHelpText(HelpText); connect(m_Controls->btnClosing, SIGNAL(clicked()), this, SLOT(OnClosingButtonClicked())); connect(m_Controls->btnOpening, SIGNAL(clicked()), this, SLOT(OnOpeningButtonClicked())); connect(m_Controls->btnDilatation, SIGNAL(clicked()), this, SLOT(OnDilatationButtonClicked())); connect(m_Controls->btnErosion, SIGNAL(clicked()), this, SLOT(OnErosionButtonClicked())); connect(m_Controls->btnFillHoles, SIGNAL(clicked()), this, SLOT(OnFillHolesButtonClicked())); connect(m_Controls->radioButtonMorphoCross, SIGNAL(clicked()), this, SLOT(OnRadioButtonsClicked())); connect(m_Controls->radioButtonMorphoBall, SIGNAL(clicked()), this, SLOT(OnRadioButtonsClicked())); connect(m_Controls->dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if (m_Controls->dataSelectionWidget->GetSelection(0).IsNotNull()) this->OnSelectionChanged(0, m_Controls->dataSelectionWidget->GetSelection(0)); } QmitkMorphologicalOperationsWidget::~QmitkMorphologicalOperationsWidget() { } void QmitkMorphologicalOperationsWidget::OnSelectionChanged(unsigned int, const mitk::DataNode*) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(0); if (node.IsNotNull()) { m_Controls->dataSelectionWidget->SetHelpText(""); this->EnableButtons(true); } else { m_Controls->dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } } void QmitkMorphologicalOperationsWidget::EnableButtons(bool enable) { m_Controls->btnClosing->setEnabled(enable); m_Controls->btnDilatation->setEnabled(enable); m_Controls->btnErosion->setEnabled(enable); m_Controls->btnFillHoles->setEnabled(enable); m_Controls->btnOpening->setEnabled(enable); } void QmitkMorphologicalOperationsWidget::OnRadioButtonsClicked() { bool enable = m_Controls->radioButtonMorphoBall->isChecked(); m_Controls->sliderMorphFactor->setEnabled(enable); m_Controls->spinBoxMorphFactor->setEnabled(enable); } void QmitkMorphologicalOperationsWidget::OnClosingButtonClicked() { QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(0); mitk::Image::Pointer image = static_cast(node->GetData()); mitk::MorphologicalOperations::StructuralElementType structuralElement = CreateStructerElement_UI(); try { int factor = m_Controls->spinBoxMorphFactor->isEnabled() ? m_Controls->spinBoxMorphFactor->value() : 1; mitk::MorphologicalOperations::Closing(image, factor, structuralElement); } catch (const itk::ExceptionObject& exception) { MITK_WARN << "Exception caught: " << exception.GetDescription(); QApplication::restoreOverrideCursor(); return; } node->SetData(image); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QApplication::restoreOverrideCursor(); } void QmitkMorphologicalOperationsWidget::OnOpeningButtonClicked() { QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(0); mitk::Image::Pointer image = static_cast(node->GetData()); mitk::MorphologicalOperations::StructuralElementType structuralElement = CreateStructerElement_UI(); try { int factor = m_Controls->spinBoxMorphFactor->isEnabled() ? m_Controls->spinBoxMorphFactor->value() : 1; mitk::MorphologicalOperations::Opening(image, factor, structuralElement); } catch (const itk::ExceptionObject& exception) { MITK_WARN << "Exception caught: " << exception.GetDescription(); QApplication::restoreOverrideCursor(); return; } node->SetData(image); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QApplication::restoreOverrideCursor(); } void QmitkMorphologicalOperationsWidget::OnDilatationButtonClicked() { QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(0); mitk::Image::Pointer image = static_cast(node->GetData()); mitk::MorphologicalOperations::StructuralElementType structuralElement = this->CreateStructerElement_UI(); try { int factor = m_Controls->spinBoxMorphFactor->isEnabled() ? m_Controls->spinBoxMorphFactor->value() : 1; mitk::MorphologicalOperations::Dilate(image, factor, structuralElement); } catch (const itk::ExceptionObject& exception) { MITK_WARN << "Exception caught: " << exception.GetDescription(); QApplication::restoreOverrideCursor(); return; } node->SetData(image); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QApplication::restoreOverrideCursor(); } void QmitkMorphologicalOperationsWidget::OnErosionButtonClicked() { QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(0); mitk::Image::Pointer image = static_cast(node->GetData()); mitk::MorphologicalOperations::StructuralElementType structuralElement = CreateStructerElement_UI(); try { int factor = m_Controls->spinBoxMorphFactor->isEnabled() ? m_Controls->spinBoxMorphFactor->value() : 1; mitk::MorphologicalOperations::Erode(image, factor, structuralElement); } catch (const itk::ExceptionObject& exception) { MITK_WARN << "Exception caught: " << exception.GetDescription(); QApplication::restoreOverrideCursor(); return; } node->SetData(image); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QApplication::restoreOverrideCursor(); } void QmitkMorphologicalOperationsWidget::OnFillHolesButtonClicked() { QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(0); mitk::Image::Pointer image = static_cast(node->GetData()); try { mitk::MorphologicalOperations::FillHoles(image); } catch (const itk::ExceptionObject& exception) { MITK_WARN << "Exception caught: " << exception.GetDescription(); QApplication::restoreOverrideCursor(); return; } node->SetData(image); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); QApplication::restoreOverrideCursor(); } mitk::MorphologicalOperations::StructuralElementType QmitkMorphologicalOperationsWidget::CreateStructerElement_UI() { bool ball = m_Controls->radioButtonMorphoBall->isChecked(); int accum_flag = 0; if(ball){ if(m_Controls->planeSelectionComboBox->currentIndex() == 0) accum_flag = mitk::MorphologicalOperations::Ball; // 3D Operation if(m_Controls->planeSelectionComboBox->currentIndex() == 1) accum_flag = mitk::MorphologicalOperations::Ball_Axial; // 2D Operation - Axial plane if(m_Controls->planeSelectionComboBox->currentIndex() == 2) accum_flag = mitk::MorphologicalOperations::Ball_Sagittal; // 2D Operation - Sagittal plane if(m_Controls->planeSelectionComboBox->currentIndex() == 3) accum_flag = mitk::MorphologicalOperations::Ball_Coronal; // 2D Operation - Coronal plane }else{ if(m_Controls->planeSelectionComboBox->currentIndex() == 0) accum_flag = mitk::MorphologicalOperations::Cross; if(m_Controls->planeSelectionComboBox->currentIndex() == 1) accum_flag = mitk::MorphologicalOperations::Cross_Axial; if(m_Controls->planeSelectionComboBox->currentIndex() == 2) accum_flag = mitk::MorphologicalOperations::Cross_Sagittal; if(m_Controls->planeSelectionComboBox->currentIndex() == 3) accum_flag = mitk::MorphologicalOperations::Cross_Coronal; } return (mitk::MorphologicalOperations::StructuralElementType)accum_flag; } diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.h b/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.h index 8267cc54e7..3d19b84668 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.h +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkMorphologicalOperationsWidget.h @@ -1,58 +1,61 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMorphologicalOperationsWidget_h #define QmitkMorphologicalOperationsWidget_h #include #include #include namespace Ui { class QmitkMorphologicalOperationsWidgetControls; } namespace mitk { class DataNode; + class DataStorage; } /** \brief GUI class for morphological segmentation tools. */ class MITKSEGMENTATIONUI_EXPORT QmitkMorphologicalOperationsWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: - explicit QmitkMorphologicalOperationsWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); + explicit QmitkMorphologicalOperationsWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent = nullptr); ~QmitkMorphologicalOperationsWidget() override; public slots: void OnClosingButtonClicked(); void OnOpeningButtonClicked(); void OnDilatationButtonClicked(); void OnErosionButtonClicked(); void OnFillHolesButtonClicked(); void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); void OnRadioButtonsClicked(); protected: void EnableButtons(bool enable); private: Ui::QmitkMorphologicalOperationsWidgetControls* m_Controls; mitk::MorphologicalOperations::StructuralElementType CreateStructerElement_UI(); }; #endif diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.cpp b/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.cpp index 095a855896..2e0edecc2f 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.cpp +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.cpp @@ -1,159 +1,170 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkSurfaceToImageWidget.h" #include +#include #include #include #include #include #include #include #include #include #include static const char* const HelpText = "Select an image and a surface above"; -QmitkSurfaceToImageWidget::QmitkSurfaceToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) +QmitkSurfaceToImageWidget::QmitkSurfaceToImageWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls = new Ui::QmitkSurfaceToImageWidgetControls; m_Controls->setupUi(this); + m_Controls->dataSelectionWidget->SetDataStorage(dataStorage); m_Controls->dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImageAndSegmentationPredicate); m_Controls->dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::SurfacePredicate); m_Controls->dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); connect (m_Controls->btnSurface2Image, SIGNAL(pressed()), this, SLOT(OnSurface2ImagePressed())); connect(m_Controls->dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if( m_Controls->dataSelectionWidget->GetSelection(0).IsNotNull() && m_Controls->dataSelectionWidget->GetSelection(1).IsNotNull() ) { this->OnSelectionChanged(0, m_Controls->dataSelectionWidget->GetSelection(0)); } } QmitkSurfaceToImageWidget::~QmitkSurfaceToImageWidget() { } void QmitkSurfaceToImageWidget::EnableButtons(bool enable) { m_Controls->btnSurface2Image->setEnabled(enable); } void QmitkSurfaceToImageWidget::OnSelectionChanged(unsigned int, const mitk::DataNode*) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer surfaceNode = dataSelectionWidget->GetSelection(1); if (imageNode.IsNull() || surfaceNode.IsNull() ) { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } else { mitk::Image::Pointer image = dynamic_cast( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Surface::Pointer surface = dynamic_cast( dataSelectionWidget->GetSelection(1)->GetData() ); if( image->GetTimeSteps() != surface->GetTimeSteps() ) { dataSelectionWidget->SetHelpText("Image and surface are of different size"); this->EnableButtons(false); } else { dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } } } void QmitkSurfaceToImageWidget::OnSurface2ImagePressed() { this->EnableButtons(false); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls->dataSelectionWidget; mitk::Image::Pointer image = dynamic_cast( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Surface::Pointer surface = dynamic_cast( dataSelectionWidget->GetSelection(1)->GetData() ); if( image.IsNull() || surface.IsNull()) { MITK_ERROR << "Selection does not contain an image and/or a surface"; QMessageBox::information( this, "Surface To Image", "Selection does not contain an image and/or a surface", QMessageBox::Ok ); this->EnableButtons(); return; } mitk::Image::Pointer resultImage(nullptr); resultImage = this->ConvertSurfaceToImage( image, surface ); if( resultImage.IsNull() ) { MITK_ERROR << "Convert Surface to binary image failed"; QMessageBox::information( this, "Surface To Image", "Convert Surface to binary image failed", QMessageBox::Ok ); this->EnableButtons(); return; } //create name for result node std::string nameOfResultImage = dataSelectionWidget->GetSelection(0)->GetName(); nameOfResultImage.append("_"); nameOfResultImage.append(dataSelectionWidget->GetSelection(1)->GetName()); //create data node and add to data storage mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); resultNode->SetData( resultImage ); resultNode->SetProperty("name", mitk::StringProperty::New(nameOfResultImage) ); // resultNode->SetProperty("binary", mitk::BoolProperty::New(true) ); - dataSelectionWidget->GetDataStorage()->Add(resultNode, dataSelectionWidget->GetSelection(0)); + auto dataStorage = dataSelectionWidget->GetDataStorage(); + if (dataStorage.IsNull()) + { + std::string exception = "Cannot add result to the data storage. Data storage invalid."; + MITK_ERROR << "Error converting surface to binary image: " << exception; + QMessageBox::information(nullptr, "Error converting surface to binary image", QString::fromStdString(exception)); + } + dataStorage->Add(resultNode, dataSelectionWidget->GetSelection(0)); this->EnableButtons(); } mitk::LabelSetImage::Pointer QmitkSurfaceToImageWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ) { mitk::ProgressBar::GetInstance()->AddStepsToDo(2); mitk::ProgressBar::GetInstance()->Progress(); mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->MakeOutputBinaryOn(); surfaceToImageFilter->SetInput(surface); surfaceToImageFilter->SetImage(image); try { surfaceToImageFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return nullptr; } mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer resultImage = surfaceToImageFilter->GetOutput(); mitk::LabelSetImage::Pointer multilabelImage = mitk::LabelSetImage::New(); multilabelImage->InitializeByLabeledImage(resultImage); return multilabelImage; } diff --git a/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.h b/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.h index 032ec3936b..55e2178163 100644 --- a/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.h +++ b/Modules/SegmentationUI/SegmentationUtilities/QmitkSurfaceToImageWidget.h @@ -1,74 +1,77 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSurfaceToImageWidget_h #define QmitkSurfaceToImageWidget_h #include #include #include "itkSmartPointer.h" namespace Ui { class QmitkSurfaceToImageWidgetControls; } namespace mitk { class DataNode; + class DataStorage; class Surface; class Image; class LabelSetImage; } /*! \brief QmitkSurfaceToImageWidget The Tool converts a surface to a binary image. The Method requires a surface and an image, which header information defines the output image. The resulting binary image has the same dimension, size, and Geometry3D as the input image. */ class MITKSEGMENTATIONUI_EXPORT QmitkSurfaceToImageWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ - explicit QmitkSurfaceToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); + explicit QmitkSurfaceToImageWidget(mitk::DataStorage* dataStorage, + mitk::SliceNavigationController* timeNavigationController, + QWidget* parent = nullptr); /** @brief Defaul destructor. */ ~QmitkSurfaceToImageWidget() override; private slots: /** @brief This slot is called if the selection in the workbench is changed. */ void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); /** @brief This slot is called if user activates the button to convert a surface into a binary image. */ void OnSurface2ImagePressed(); private: /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Convert a surface into an binary image. */ itk::SmartPointer ConvertSurfaceToImage( itk::SmartPointer image, itk::SmartPointer surface ); Ui::QmitkSurfaceToImageWidgetControls* m_Controls; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationUtilitiesView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationUtilitiesView.cpp index 5b5d5876e6..330e893f69 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationUtilitiesView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationUtilitiesView.cpp @@ -1,85 +1,86 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkSegmentationUtilitiesView.h" #include #include #include #include #include QmitkSegmentationUtilitiesView::QmitkSegmentationUtilitiesView() : m_BooleanOperationsWidget(nullptr), m_ContourModelToImageWidget(nullptr), m_ImageMaskingWidget(nullptr), m_MorphologicalOperationsWidget(nullptr), m_SurfaceToImageWidget(nullptr) { } QmitkSegmentationUtilitiesView::~QmitkSegmentationUtilitiesView() { } void QmitkSegmentationUtilitiesView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); mitk::SliceNavigationController* timeNavigationController = renderWindowPart != nullptr ? renderWindowPart->GetTimeNavigationController() : nullptr; - m_BooleanOperationsWidget = new QmitkBooleanOperationsWidget(timeNavigationController, parent); - m_ContourModelToImageWidget = new QmitkContourModelToImageWidget(timeNavigationController, parent); - m_ImageMaskingWidget = new QmitkImageMaskingWidget(timeNavigationController, parent); - m_MorphologicalOperationsWidget = new QmitkMorphologicalOperationsWidget(timeNavigationController, parent); - m_SurfaceToImageWidget = new QmitkSurfaceToImageWidget(timeNavigationController, parent); + auto dataStorage = this->GetDataStorage(); + m_BooleanOperationsWidget = new QmitkBooleanOperationsWidget(dataStorage, timeNavigationController, parent); + m_ContourModelToImageWidget = new QmitkContourModelToImageWidget(dataStorage, timeNavigationController, parent); + m_ImageMaskingWidget = new QmitkImageMaskingWidget(dataStorage, timeNavigationController, parent); + m_MorphologicalOperationsWidget = new QmitkMorphologicalOperationsWidget(dataStorage, timeNavigationController, parent); + m_SurfaceToImageWidget = new QmitkSurfaceToImageWidget(dataStorage, timeNavigationController, parent); this->AddUtilityWidget(m_BooleanOperationsWidget, QIcon(":/SegmentationUtilities/BooleanOperations_48x48.png"), "Boolean Operations"); this->AddUtilityWidget(m_ContourModelToImageWidget, QIcon(":/SegmentationUtilities/ContourModelSetToImage_48x48.png"), "Contour to Image"); this->AddUtilityWidget(m_ImageMaskingWidget, QIcon(":/SegmentationUtilities/ImageMasking_48x48.png"), "Image Masking"); this->AddUtilityWidget(m_MorphologicalOperationsWidget, QIcon(":/SegmentationUtilities/MorphologicalOperations_48x48.png"), "Morphological Operations"); this->AddUtilityWidget(m_SurfaceToImageWidget, QIcon(":/SegmentationUtilities/SurfaceToImage_48x48.png"), "Surface to Image"); } void QmitkSegmentationUtilitiesView::AddUtilityWidget(QWidget* widget, const QIcon& icon, const QString& text) { m_Controls.toolBox->addItem(widget, icon, text); } void QmitkSegmentationUtilitiesView::SetFocus() { m_Controls.toolBox->setFocus(); } void QmitkSegmentationUtilitiesView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { mitk::SliceNavigationController* timeNavigationController = renderWindowPart->GetTimeNavigationController(); m_BooleanOperationsWidget->SetTimeNavigationController(timeNavigationController); m_ContourModelToImageWidget->SetTimeNavigationController(timeNavigationController); m_ImageMaskingWidget->SetTimeNavigationController(timeNavigationController); m_MorphologicalOperationsWidget->SetTimeNavigationController(timeNavigationController); m_SurfaceToImageWidget->SetTimeNavigationController(timeNavigationController); } void QmitkSegmentationUtilitiesView::RenderWindowPartDeactivated(mitk::IRenderWindowPart*) { m_BooleanOperationsWidget->SetTimeNavigationController(nullptr); m_ContourModelToImageWidget->SetTimeNavigationController(nullptr); m_ImageMaskingWidget->SetTimeNavigationController(nullptr); m_MorphologicalOperationsWidget->SetTimeNavigationController(nullptr); m_SurfaceToImageWidget->SetTimeNavigationController(nullptr); }